def __init__(self, pairs, numbers, orders=None):
"""Initialize a molecular graph
Arguments:
pairs -- See base class (Graph) documentation
numbers -- consecutive atom numbers
orders -- bond orders
When the nature of an atom or a bond is unclear ambiguous, set the
corresponding integer to zero. This means the nature of the atom or bond
is unspecified. When the bond orders are not given, they are all set to
zero.
If you want to use 'special' atom types, use negative numbers. The same
for bond orders. e.g. a nice choice for the bond order of a hybrid bond
is -1.
"""
if orders is None:
orders = numpy.zeros(len(pairs), dtype=int)
elif len(orders) != len(pairs):
raise ValueError("The number of (bond) orders must be equal to the number of pairs")
Graph.__init__(self, pairs, len(numbers))
self._numbers = numpy.array(numbers)
self._numbers.setflags(write=False)
self._orders = numpy.array(orders)
self._orders.setflags(write=False)
def __init__(self, edges, numbers, orders=None, symbols=None, num_vertices=None):
"""
Arguments:
| ``edges`` -- See base class (Graph) documentation
| ``numbers`` -- consecutive atom numbers
Optional arguments:
| ``orders`` -- bond orders
| ``symbols`` -- atomic symbols
| ``num_vertices`` -- must be the same as the number of atoms or None
When the nature of an atom or a bond is unclear ambiguous, set the
corresponding integer to zero. This means the nature of the atom or
bond is unspecified. When the bond orders are not given, they are all
set to zero.
If you want to use 'special' atom types, use negative numbers. The
same for bond orders. e.g. a nice choice for the bond order of a
hybrid bond is -1.
"""
if num_vertices is not None and num_vertices != len(numbers):
raise ValueError('The number of vertices must be the same as the number of atoms.')
if orders is None:
orders = numpy.ones(len(edges), float)
Graph.__init__(self, edges, len(numbers))
self.numbers = numbers
self.orders = orders
self.symbols = symbols
def __init__(self,
edges,
numbers,
orders=None,
symbols=None,
num_vertices=None):
"""
Arguments:
| ``edges`` -- See base class (Graph) documentation
| ``numbers`` -- consecutive atom numbers
Optional arguments:
| ``orders`` -- bond orders
| ``symbols`` -- atomic symbols
| ``num_vertices`` -- must be the same as the number of atoms or None
When the nature of an atom or a bond is unclear ambiguous, set the
corresponding integer to zero. This means the nature of the atom or
bond is unspecified. When the bond orders are not given, they are all
set to zero.
If you want to use 'special' atom types, use negative numbers. The
same for bond orders. e.g. a nice choice for the bond order of a
hybrid bond is -1.
"""
if num_vertices is not None and num_vertices != len(numbers):
raise ValueError(
'The number of vertices must be the same as the number of atoms.'
)
if orders is None:
orders = np.ones(len(edges), float)
Graph.__init__(self, edges, len(numbers))
self.numbers = numbers
self.orders = orders
self.symbols = symbols
